Research workbench
D170N variant of beta-phosphoglucomutase from lactococcus lactis in an open conformer to 1.4 a.
Analyse D170N variant of beta-phosphoglucomutase from lactococcus lactis in an open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDF
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- NA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 219 | 54% helix, 11% strand | P71447 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.71 | 0.79 | 55 | EDO |
| 2 | 680 | 0.70 | 0.77 | 52 | EDO |
Interfaces
1 interface between chains.
- A–B · 571 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6HDF · D170N variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to… · the same entry in another collection · chain A against A, TM-score 1.00
- P71447 · AlphaFold monomer V2.0 prediction for beta-phosphoglucomutase (P71447) · a predicted model of the same protein · chain A against A, TM-score 0.86
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P71447
- Elsewhere: RCSB PDB 6HDF · PDBe 6HDF · UniProt P71447
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